rs2297328
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Variant summary
Our verdict is Benign. Variant got -13 ACMG points: 0P and 13B. BP4_StrongBP7BA1
The NM_019590.5(KIAA1217):āc.2532A>Gā(p.Thr844=) variant causes a synonymous change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0614 in 1,614,102 control chromosomes in the GnomAD database, including 5,210 homozygotes. In-silico tool predicts a benign outcome for this variant. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar.
Frequency
Genomes: š 0.12 ( 1698 hom., cov: 33)
Exomes š: 0.056 ( 3512 hom. )
Consequence
KIAA1217
NM_019590.5 synonymous
NM_019590.5 synonymous
Scores
2
Clinical Significance
Not reported in ClinVar
Conservation
PhyloP100: -4.34
Genes affected
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ACMG classification
Classification made for transcript
Verdict is Benign. Variant got -13 ACMG points.
BP4
?
Computational evidence support a benign effect (BayesDel_noAF=-0.9).
BP7
?
Synonymous conserved (PhyloP=-4.34 with no splicing effect.
BA1
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GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.263 is higher than 0.05.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
KIAA1217 | NM_019590.5 | c.2532A>G | p.Thr844= | synonymous_variant | 13/21 | ENST00000376454.8 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
KIAA1217 | ENST00000376454.8 | c.2532A>G | p.Thr844= | synonymous_variant | 13/21 | 1 | NM_019590.5 | A2 |
Frequencies
GnomAD3 genomes ? AF: 0.115 AC: 17462AN: 152142Hom.: 1679 Cov.: 33
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GnomAD3 exomes AF: 0.0810 AC: 20346AN: 251338Hom.: 1345 AF XY: 0.0758 AC XY: 10291AN XY: 135848
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GnomAD4 exome AF: 0.0558 AC: 81539AN: 1461842Hom.: 3512 Cov.: 31 AF XY: 0.0554 AC XY: 40263AN XY: 727222
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GnomAD4 genome ? AF: 0.115 AC: 17512AN: 152260Hom.: 1698 Cov.: 33 AF XY: 0.116 AC XY: 8628AN XY: 74474
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ClinVar
Not reported inComputational scores
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Name
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BayesDel_noAF
Benign
CADD
Benign
DANN
Benign
Splicing
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Details are displayed if max score is > 0.2
Find out detailed SpliceAI scores and Pangolin per-transcript scores at